Modelpublic

PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v2.1

sourceHugging Facemitupdated 2y agoView on Hugging Face

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Model Card

Feature	Description
Name	`BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1`
Default Pipeline	`transformer`, `ner`
Components	`transformer`, `ner`
Vectors	0 keys, 0 unique vectors (0 dimensions)
Sources	n/a
License	n/a
Author	[Melanie Vollmar]()

Label Scheme

<summary>View label scheme (20 labels for 1 components)</summary>

Component	Labels
`ner`	"bondinteraction", "chemical", "complexassembly", "evidence", "experimentalmethod", "gene", "mutant", "oligomericstate", "protein", "proteinstate", "proteintype", "ptm", "residuename", "residuenamenumber", "residuenumber", "residuerange", "site", "species", "structureelement", "taxonomy_domain"

</details>

Scores for entity types

entity type	precision	recall	F1	sample number
"bond_interaction"	0.93	0.88	0.90	43
"chemical"	0.89	0.91	0.90	761
"complex_assembly"	0.91	0.93	0.92	288
"evidence"	0.84	0.88	0.86	390
"experimental_method"	0.85	0.85	0.85	357
"gene"	0.79	0.86	0.82	43
"mutant"	0.91	0.97	0.94	463
"oligomeric_state"	0.93	0.99	0.96	142
"protein"	0.94	0.97	0.95	1411
"protein_state"	0.83	0.88	0.85	546
"protein_type"	0.85	0.85	0.85	414
"ptm"	0.70	0.70	0.70	50
"residue_name"	0.92	0.97	0.94	90
"residuenamenumber"	0.95	0.96	0.96	561
"residue_number"	0.80	0.97	0.88	33
"residue_range"	0.81	0.70	0.75	43
"site"	0.85	0.87	0.86	270
"species"	0.94	0.96	0.95	84
"structure_element"	0.91	0.92	0.92	992
"taxonomy_domain"	0.99	0.98	0.98	88

Data and annotations

The dataset can be found here: https://huggingface.co/datasets/PDBEurope/proteinstructureNERmodelv2.1

Citation

Vollmar, M., Tirunagari, S., Harrus, D. et al. Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature. Sci Data 11, 1032 2024 https://doi.org/10.1038/s41597-024-03841-9